Phylogeny, Molecules Versus Morphology, and Rates of Character Evolution Among Fruitbats (Chiroptera: Megachiroptera)

1995 ◽  
Vol 43 (6) ◽  
pp. 557 ◽  
Author(s):  
MS Springer ◽  
LJ Hollar ◽  
JAW Kirsch
Keyword(s):  
Cladistic Analysis ◽  
Strong Support ◽  
Morphological Characters ◽  
Character Evolution ◽  
Morphological Data ◽  
Phylogenetic Position ◽  
Minimum Length ◽  
Data Set ◽  
Dna Hybridisation ◽  
Phylogenetic Hypotheses

Andersen's 1912 monograph on megachiropterans remains the definitive work on the systematics of this group. Andersen argued that the Macroglossinae, containing the eonycterine and notopterine sections, are a monophyletic sister-group to other fruitbats (i.e. Andersen's Rousettus, Cynopterus and Epomophorus sections). Two recent molecular studies (DNA hybridisation and restriction mapping of ribosomal cistrons), as well as an analysis of female reproductive characters, challenge the monophyly of the Macroglossinae and several of Andersen's other conclusions such as the phylogenetic position of Nyctimene. We performed a cladistic analysis on 36 morphological characters, including 33 that were gleaned from Andersen, to determine whether phylogenetic hypotheses based on modem phylogenetic methods are in agreement with Andersen's original conclusions and to compare morphological and molecular phylogenetic hypotheses. Minimum-length trees based on parsimony are largely consistent with Andersen and support (1) a monophyletic Macroglossinae, within which the eonycterine section is paraphyletic with respect to a monophyletic notopterine section, (2) a monophyletic Cynopterus section, excepting the exclusion of Myonycteris, (3) a monophyletic Epomophorus section, excepting the exclusion of Plerotes, and (4) a paraphyletic Rousettus section, with several of the Rousettus-like forms branching off near the base of the tree. Bootstrapping analyses on a reduced data-set that included taxa shared in common with the DNA hybridisation study did not provide strong support (greater than or equal to 95%) for any clades but did provide moderate support (greater than or equal to 70) for several clades, including a monophyletic Macroglossinae. These findings are in marked contrast to the DNA hybridisation phylogeny. A high index of between-data-set incongruence is further evidence for the clash between DNA hybridisation and morphology. A phylogenetic framework was constructed on the basis of morphological data and DNA hybridisation data using a criterion of moderate support and shows little resolution, whereas employing a criterion of strong support produced a framework resolving several additional nodes. One implication of this framework is that characteristic macroglossine features such as a long tongue with a thick carpet of filiform papillae have evolved independently on several occasions (or evolved once and were lost several times). Rates of character evolution for the morphological characters employed in our analysis were calculated using divergence times estimated from DNA hybridisation data. Rates have apparently been fastest in the interior branches, and slower along the external branches, which suggests an early adaptive radiation in the history of fruitbats.

scholarly journals Phylogenetic Position of the New World Quail (Odontophoridae): Eight Nuclear Loci and Three Mitochondrial Regions Contradict Morphology and the Sibley-Ahlquist Tapestry

The Auk ◽  
2007 ◽  
Vol 124 (1) ◽  
pp. 71-84 ◽  
Author(s):  
W. Andrew Cox ◽  
Rebecca T. Kimball ◽  
Edward L. Braun
Keyword(s):  
New World ◽  
Sequence Data ◽  
Evolutionary Relationship ◽  
Strong Support ◽  
Nuclear Data ◽  
Morphological Data ◽  
Phylogenetic Position ◽  
Data Set ◽  
Mitochondrial Data ◽  
Nuclear Loci

Abstract The evolutionary relationship between the New World quail (Odontophoridae) and other groups of Galliformes has been an area of debate. In particular, the relationship between the New World quail and guineafowl (Numidinae) has been difficult to resolve. We analyzed >8 kb of DNA sequence data from 16 taxa that represent all major lineages of Galliformes to resolve the phylogenetic position of New World quail. A combined data set of eight nuclear loci and three mitochondrial regions analyzed with maximum parsimony, maximum likelihood, and Bayesian methods provide congruent and strong support for New World quail being basal members of a phasianid clade that excludes guineafowl. By contrast, the three mitochondrial regions exhibit modest incongruence with each other. This is reflected in the combined mitochondrial analyses that weakly support the Sibley-Ahlquist topology that placed the New World quail basal in relation to guineafowl and led to the placement of New World quail in its own family, sister to the Phasianidae. However, simulation-based topology tests using the mitochondrial data were unable to reject the topology suggested by our combined (mitochondrial and nuclear) data set. By contrast, similar tests using our most likely topology and our combined nuclear and mitochondrial data allow us to strongly reject the Sibley-Ahlquist topology and a topology based on morphological data that unites Old and New World quail. Posición Filogenética de las Codornices del Nuevo Mundo (Odontophoridae): Ocho Loci Nucleares y Tres Regiones Mitocondriales Contradicen la Morfología y la Filogenia de Sibley y Ahlquist

A cladistic analysis of Trombidiidae (Acari: Parasitengona): congruence of larval and adult character sets

1995 ◽  
Vol 73 (1) ◽  
pp. 96-103 ◽  
Author(s):  
Zhi-Qiang Zhang
Keyword(s):  
Cladistic Analysis ◽  
Morphological Characters ◽  
Total Evidence ◽  
Morphological Data ◽  
Data Sets ◽  
Parsimony Analysis ◽  
Data Set ◽  
Clade B ◽  
Generic Relationships ◽  
Combined Data

Two morphological data sets for eight trombidioid genera (Acari: Parasitengona) were analyzed separately and in combination using cladistic methods. One data set comprised 15 adult morphological characters, whereas the other comprised 29 larval morphological characters. Analyzed separately, the data on adults produced five equally parsimonious trees and the data on larvae produced three equally parsimonious trees. Analyses of both data sets revealed two distinct clades in Trombidiidae: clade A (Podothrombium, Pollicotrombium, Paratrombium, and Trombidium) and clade B (Dinothrombium, Clinotrombium, and Allothrombium). However, the within-clade generic relationships were resolved by data from larvae only in clade A and by data from adults only in clade B. Analysis of the combined data produced a single most parsimonious tree, with both clade A (Podothrombium (Pollicotrombium (Paratrombium, Trombidium))) and clade B (Dinothrombium (Clinotrombium, Allothrombium)) completely resolved. Thus, data on larvae and postlarvae are not only congruent but also complementary in revealing the phylogenetic relationships of these mites. The results support the principle of total evidence and the use of all available data for a single parsimony analysis.

Taxonomic review and cladistic analysis of Neotropical spider genus Epicratinus Jocqué & Baert, 2005 (Araneae: Zodariidae) with description of eleven new species

Zootaxa ◽  
2020 ◽  
Vol 4886 (1) ◽  
pp. 1-77
Author(s):  
RICARDO ANTONIO GONÇALVES ◽  
ANTONIO DOMINGOS BRESCOVIT
Keyword(s):  
Phylogenetic Analysis ◽  
Cladistic Analysis ◽  
Taxonomic Revision ◽  
Morphological Characters ◽  
Morphological Data ◽  
Data Set ◽  
Distribution Maps ◽  
Character Weighting ◽  
Males And Females ◽  
First Time

A taxonomic revision and phylogenetic analysis of the spider genus Epicratinus Jocqué & Baert, 2005 is presented. The phylogenetic analysis is based on a data set including 16 Epicratinus species plus 9 outgroups representing by five related zodariid gen­era and one of them considered most basal as the root. These taxa were scored for 49 morphological characters. Parsimony was used as the op­timality criterion and a sensitivity analysis was performed using different character weighting concavities. Five unambiguous synapomorphies support the monophyly of Epicratinus. Some internal clades within the genus are well-supported and their relationships are discussed. Epicratinus includes 16 species, all with males and females. A species identification key and distribution maps are provided for all. New morphological data are also pre­sented for five previously described species. All 16 species occur only in the New World. The following species are transferred to Epicratinus: E. perfidus (Jocqué & Baert), comb. nov. from Tenedos; Epicratinus perfidus Jocqué & Baert comb. nov. and newly synonymized with E. santacruz Grismado & Izquierdo and this last species is treated as the junior synonym. Epicratinus petropolitanus (Mello-Leitão) has the male described for the first time. The following 11 species are newly described as new: E. zangief sp. nov.; E. pegasus sp. nov.; E. pikachu sp. nov.; E. stitch sp. nov.; E. ehonda sp. nov.; E. anakin sp. nov.; E. vader sp. nov.; E. omegarugal sp. nov.; E. zelda sp. nov.; E. dookan sp. nov. and E. mauru sp. nov., all from Brazil. 

Is Elsiella Froeschner, 1981 a valid genus? (Hemiptera: Heteroptera: Pentatomidae: Pentatominae)

Zootaxa ◽  
2012 ◽  
Vol 3238 (1) ◽  
pp. 39 ◽  
Author(s):  
FELIPE LORENZ SIMÕES ◽  
AUGUSTO FERRARI ◽  
JOCÉLIA GRAZIA
Keyword(s):  
Cladistic Analysis ◽  
Morphological Characters ◽  
Data Set ◽  
Male Specimen ◽  
Valid Genus ◽  
Heteroptera Pentatomidae

The genus Elsiella Froeschner, 1981 is validated based on the analysis of a recently found male specimen of E. plana(Walker, 1867). A cladistic analysis comprising a data set of 40 morphological characters and 22 taxa, including the generaElsiella, Serdia Stål, Similliserdia Fortes & Grazia, Neotibilis Grazia & Barcellos, and Tibilis Stål, was performed. Elsiellaplana is redescribed and illustrated. Maps are provided for Elsiella and Serdia with biogeographical considerations for Serdia.

scholarly journals Intergeneric Relationships within the Early-Diverging Angiosperm Family Nymphaeaceae Based on Chloroplast Phylogenomics

2018 ◽  
Vol 19 (12) ◽  
pp. 3780 ◽  
Author(s):  
Dingxuan He ◽  
Andrew Gichira ◽  
Zhizhong Li ◽  
John Nzei ◽  
Youhao Guo ◽  
...  
Keyword(s):  
Genome Structure ◽  
Morphological Data ◽  
Basal Angiosperm ◽  
Phylogenetic Position ◽  
Data Set ◽  
Protein Coding ◽  
Plastid Genomes ◽  
Chloroplast Genomes ◽  
Gene Data ◽  
High Degree

The order Nymphaeales, consisting of three families with a record of eight genera, has gained significant interest from botanists, probably due to its position as a basal angiosperm. The phylogenetic relationships within the order have been well studied; however, a few controversial nodes still remain in the Nymphaeaceae. The position of the Nuphar genus and the monophyly of the Nymphaeaceae family remain uncertain. This study adds to the increasing number of the completely sequenced plastid genomes of the Nymphaeales and applies a large chloroplast gene data set in reconstructing the intergeneric relationships within the Nymphaeaceae. Five complete chloroplast genomes were newly generated, including a first for the monotypic Euryale genus. Using a set of 66 protein-coding genes from the chloroplast genomes of 17 taxa, the phylogenetic position of Nuphar was determined and a monophyletic Nymphaeaceae family was obtained with convincing statistical support from both partitioned and unpartitioned data schemes. Although genomic comparative analyses revealed a high degree of synteny among the chloroplast genomes of the ancient angiosperms, key minor variations were evident, particularly in the contraction/expansion of the inverted-repeat regions and in RNA-editing events. Genome structure, and gene content and arrangement were highly conserved among the chloroplast genomes. The intergeneric relationships defined in this study are congruent with those inferred using morphological data.

The systematics of Raspailiidae (Demospongiae: Poecilosclerida: Microcionina) re-analysed with a ribosomal marker

2007 ◽  
Vol 87 (6) ◽  
pp. 1571-1576 ◽  
Author(s):  
Dirk Erpenbeck ◽  
Sue List-Armitage ◽  
Belinda Alvarez ◽  
Bernard M. Degnan ◽  
Gert Wörheide ◽  
...  
Keyword(s):  
Gene Tree ◽  
Morphological Characters ◽  
Character Evolution ◽  
28S Rdna ◽  
The Other ◽  
Data Set ◽  
Rdna Gene ◽  
Insight Into

We present a 28S rDNA gene tree of selected Raspailiidae, Axinellidae and other demosponges to obtain insight into raspailiid phylogeny and character evolution. The Raspailiidae in our data set cluster in a well-supported clade, distinguished from Axinellidae, Agelasida and Hadromerida. Raspailia (s.s.), Eurypon, Sollasella, Aulospongus and Ectyoplasia form a Raspailiidae clade. Some Raspailia subgenera, in particular R. (Parasyringella), are not retrieved monophyletically. Trikentrion falls into the Thrinacophorinae, and not the Cyamoninae as earlier hypothesized. The axinellid genera Ptilocaulis and Reniochalina also cluster with Raspailiidae, distant from the other Axinellidae. The suitability of particular morphological characters for raspailiid phylogeny is discussed.

scholarly journals Random Sequencing of Paramecium Somatic DNA

2002 ◽  
Vol 1 (3) ◽  
pp. 341-352 ◽  
Author(s):  
Linda Sperling ◽  
Philippe Dessen ◽  
Marek Zagulski ◽  
Ron E. Pearlman ◽  
Andrzey Migdalski ◽  
...  
Keyword(s):  
Germ Line ◽  
Gene Discovery ◽  
Strong Support ◽  
Distance Matrix ◽  
Sexual Cycle ◽  
Phylogenetic Position ◽  
Paramecium Tetraurelia ◽  
Data Set ◽  
Somatic Genome ◽  
Random Survey

ABSTRACT We report a random survey of 1 to 2% of the somatic genome of the free-living ciliate Paramecium tetraurelia by single-run sequencing of the ends of plasmid inserts. As in all ciliates, the germ line genome of Paramecium (100 to 200 Mb) is reproducibly rearranged at each sexual cycle to produce a somatic genome of expressed or potentially expressed genes, stripped of repeated sequences, transposons, and AT-rich unique sequence elements limited to the germ line. We found the somatic genome to be compact (>68% coding, estimated from the sequence of several complete library inserts) and to feature uniformly small introns (18 to 35 nucleotides). This facilitated gene discovery: 722 open reading frames (ORFs) were identified by similarity with known proteins, and 119 novel ORFs were tentatively identified by internal comparison of the data set. We determined the phylogenetic position of Paramecium with respect to eukaryotes whose genomes have been sequenced by the distance matrix neighbor-joining method by using random combined protein data from the project. The unrooted tree obtained is very robust and in excellent agreement with accepted topology, providing strong support for the quality and consistency of the data set. Our study demonstrates that a random survey of the somatic genome of Paramecium is a good strategy for gene discovery in this organism.

Corrigendum to: Cladistic analysis and revision of Piestus Gravenhorst with remarks on related genera (Coleoptera : Staphylinidae : Piestinae)

2013 ◽  
Vol 27 (1) ◽  
pp. 129
Author(s):  
Edilson Caron ◽  
Cibele S. Ribeiro-Costa ◽  
Alfred F. Newton
Keyword(s):  
Cladistic Analysis ◽  
Taxonomic Revision ◽  
Sister Group ◽  
Morphological Characters ◽  
Valid Species ◽  
Phylogenetic Position ◽  
Neotropical Forests ◽  
Rove Beetles ◽  
New Synonyms ◽  
Branch Support

Rove beetles of the genus Piestus Gravenhorst, 1806 are commonly captured under the bark of or inside decaying logs from Neotropical forests. Piestus belongs to the subfamily Piestinae, historically an ill-defined dumping-ground for Staphylinidae defined by plesiomorphic characters, but which has gradually been restricted in concept and currently includes only six additional extant genera worldwide. Piestinae in this restricted sense has been considered a probably monophyletic subfamily, but its status and phylogenetic position, as a possible sister-group of Osoriinae within the recently proposed Oxyteline group of staphylinid subfamilies, are uncertain and need confirmation. The main aim of the present study was to provide a morphological cladistic analysis and complete taxonomic revision of Piestus, which, as the type and most speciose genus of Piestinae, is critical for future phylogenetic studies involving the subfamily. In our study, the monophyly of Piestus is established and phylogenetic relationships among its species are proposed based on 70 adult morphological characters. Piestus is supported by 11 synapomorphies and high branch support. All species of Piestus are revised and the genus is redefined. The genus contains 43 species, including 13 species described here for the first time. The previously proposed subgenera Antropiestus Bernhauer, 1917, Eccoptopiestus Scheerpeltz, 1952, Elytropiestus Scheerpeltz, 1952, Lissopiestus Scheerpeltz, 1952, Piestus s. str., Trachypiestus Scheerpeltz, 1952 and Zirophorus Dalman, 1821 have not been confirmed, as they were found to be poly- or paraphyletic, or are here removed from Piestus, and therefore subgenera are not used. The main taxonomic changes are as follows. Lissopiestus, syn. nov. is proposed as new synonym of Eleusis Laporte, 1835 and its species, E. interrupta (Erichson, 1840), comb. rest., is transferred again to that genus. Antropiestus, syn. nov. and Eccoptopiestus, syn. nov. are proposed as new synonyms of Hypotelus Erichson, 1839 and their species, H. laevis (Solsky, 1872), comb. nov. and H. andinus (Bernhauer, 1917), comb. nov., are transferred to Hypotelus. Fourteen new synonymies are proposed (valid species listed first): P. lacordairei Laporte, 1835 = Z. furcatus Sharp, 1887, syn. nov.; P. capricornis Laporte, 1835 = P. frontalis Sharp, 1876, syn. nov.; P. pennicornis Fauvel, 1864 = P. plagiatus Fauvel, 1864, syn. nov.; P. rectus Sharp, 1876, syn. nov.; P. pygialis Fauvel, 1902, syn. nov.; P. surinamensis Bernhauer, 1928, syn. nov.; P. minutus Erichson, 1840 = P. nigrator Fauvel, 1902, syn. nov.; P. sulcatus Gravenhorst, 1806 = P. sanctaecatharinae Bernhauer, 1906, syn. nov.; P. condei Wendeler, 1955, syn. nov.; P. gounellei Fauvel, 1902 = P. wasmanni Fauvel, 1902, syn. nov.; P. mexicanus Laporte, 1835 = P. alternans Sharp, 1887, syn. nov.; P. aper Sharp, 1876 = P. schadei Scheerpeltz, 1952, syn. nov.; P. angularis Fauvel, 1864 = P. crassicornis Sharp, 1887, syn. nov.; H. andinus (Bernhauer, 1917) = P. strigipennis Bernhauer, 1921, syn. nov. One species is revalidated: P. fronticornis (Dalman, 1821), stat. rev., and one synonym is restored: P. penicillatus (Dalman, 1821) = P. erythropus Erichson, 1840, syn. rest. Neotypes are designated for P. lacordairei Laporte, 1835 and Oxytelus bicornis Olivier, 1811, and lectotypes are designated for P. puncticollis Fauvel, 1902, P. capricornis variety muticus Fauvel, 1902, P. zischkai Scheerpeltz, 1951, P. pennicornis Fauvel, 1864, P. plagiatus Fauvel, 1864, P. pygmaeus Laporte, 1835, P. niger Fauvel 1864, P. minutus Erichson, 1840, P. nigratror Fauvel, 1902, P. sulcatus Gravenhorst, 1806, P. sanctaecatharinae Bernhauer, 1906, P. sulcipennis Scheerpeltz, 1952, P. aper Sharp, 1876, P. schadei Scheerpeltz, 1952 and P. andinus Bernhauer, 1917.

scholarly journals Importance of the postcranial skeleton in eusuchian phylogeny: Reassessing the systematics of allodaposuchid crocodylians

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0251900
Author(s):  
Alejandro Blanco
Keyword(s):  
Current Knowledge ◽  
Phylogenetic Signal ◽  
Morphological Data ◽  
Phylogenetic Position ◽  
Postcranial Skeleton ◽  
Skull Morphology ◽  
Taxonomic Descriptions ◽  
The Family ◽  
Phylogenetic Hypotheses ◽  
Internal Relationships

Our current knowledge on the crocodyliform evolution is strongly biased towards the skull morphology, and the postcranial skeleton is usually neglected in many taxonomic descriptions. However, it is logical to expect that it can contribute with its own phylogenetic signal. In this paper, the changes in the tree topology caused by the addition of the postcranial information are analysed for the family Allodaposuchidae, the most representative eusuchians in the latest Cretaceous of Europe. At present, different phylogenetic hypotheses have been proposed for this group without reaching a consensus. The results of this paper evidence a shift in the phylogenetic position when the postcranium is included in the dataset, pointing to a relevant phylogenetic signal in the postcranial elements. Finally, the phylogenetic relationships of allodaposuchids within Eusuchia are reassessed; and the internal relationships within Allodaposuchidae are also reconsidered after an exhaustive revision of the morphological data. New and improved diagnoses for each species are here provided.

scholarly journals Towards a phylogeny of the Metazoa: evaluating alternative phylogenetic positions of Platyhelminthes, Nemertea, and Gnathostomulida, with a critical reappraisal of cladistic characters

2004 ◽  
Vol 73 (1-2) ◽  
pp. 3-163 ◽  
Author(s):  
Ronald A. Jenner
Keyword(s):  
Sister Group ◽  
Morphological Characters ◽  
Total Evidence ◽  
Morphological Data ◽  
Future Research ◽  
Sister Group Relationship ◽  
Cladistic Analyses ◽  
Phylogenetic Hypotheses ◽  
Data Matrices

This paper critically assesses all morphological cladistic analyses of the Metazoa that were published during the last one and a half decades. Molecular and total evidence analyses are also critically reviewed. This study focuses on evaluating alternative phylogenetic positions of the ‘acoelomate’ worms: Platyhelminthes, Nemertea, and Gnathostomulida. This paper consists of two parts. In Part I, all recently proposed sister group hypotheses and the supporting synapomorphies for these phyla are evaluated. Discrepancies in the treatment of corresponding characters in different cladistic analyses are identified, and where possible, resolved. In Part II, the overall phylogenetic significance across the Metazoa of all characters relevant for placing the ‘acoelomate’ worms is examined. The coding and scoring of these characters for other phyla are evaluated, and uncertainties in our understanding are pointed out in order to guide future research. The characters discussed in this paper are broadly categorized as follows: epidermis and cuticle, reproduction and sexual condition, development, larval forms, coeloms and mesoderm source, nervous system and sensory organs, nephridia, musculature, digestive system, and miscellaneous characters. Competing phylogenetic hypotheses are compared in terms of several criteria: 1) taxon sampling and the fulfillment of domain of definition for each character; 2) character sampling; 3) character coding; 4) character scoring and quality of primary homology; 5) quality of the proposed diagnostic synapomorphies as secondary homologies. On the basis of this study I conclude that a sister group for the Platyhelminthes has not yet been unambiguously established. A clade minimally composed of Neotrochozoa (Mollusca, Sipuncula, Echiura, Annelida) emerges as the most likely sister group of the Nemertea on the basis of morphological and total evidence analyses. Finally, morphological data currrently favor a sister group relationship of Gnathostomulida and Syndermata (probably plus Micrognathozoa). In contrast, molecular or total evidence analyses have not identified a reliable sister group of Gnathostomulida.Further progress in our understanding of metazoan phylogeny crucially depends on the improvement of the quality of currently adopted cladistic data matrices. A thorough reassessment of many of the more than 70 morphological characters discussed here is necessary. Despite the recent compilation of comprehensive data matrices, the power to test competing hypotheses of higher-level metazoan relationships is critically compromised due to uncritical data selection and poor character study in even the most recently published cladistic analyses.

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